Link learns the story through memories, but then everyone in the game is still like, "I saw Zelda! Why did she tell us to do this weird thing?" Even though it's super obvious that wasn't the real Zelda.
I kinda wish I had to figure something out to rescue Zelda rather than Rauru and Sonia just doing magic after I killed the Demon King. Why didn't they do that earlier? Obviously, I needed the dragon to fight the Demon King, but how could they know he would do what he did?
It would have been neat if there were a "bad" ending and a "good" ending where you could beat the Demon King, but if you didn't solve some larger puzzle, then you don't rescue Zelda.
I feel like they did Zelda's character dirty. You can't leave her alone for 5 minutes before she starts eating whatever weird rocks she finds on the ground.
I was incredibly on board with the main premise of the game, and had a great time with the story. I can see how others wouldn't be too impressed with it, as it's still somewhat basic compared to other games in the series, but I was completely sold by Zelda's characterization and story arc. Plus, I didn't actively hate any of the sages, which is a huge plus.
Rauru was a standout new character for me. Dude's an absolute beast, especially in the memory you get from the spirit dungeon. Ganon was fine, played very well by Matt Mercer, but I kinda wanted him more involved in the story.
Anyways, the story felt incredibly emotionally satisfying by the end. Which isn't something I can say for Breath of the Wild's story (though BotW had its moments).